galaxy main tool shed "join" installation error
Hi, I am trying to install "join" de21bdbb8d28, from Galaxy main tool shed, but it failed with the following error:
Will skip URL https://pypi.python.org/simple/numpy/1.7.1 when looking for download links for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
Will skip URL https://pypi.python.org/simple/numpy/ when looking for download links for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
Could not find any downloads that satisfy the requirement numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
No distributions at all found for numpy==1.7.1 (from -r /home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt (line 2))
Storing complete log in /home/wang/.pip/pip.log
Could not fetch URL https://pypi.python.org/simple/numpy/: There was a problem confirming the ssl certificate: <urlopen error [Errno 1] _ssl.c:497: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed>
Traceback (most recent call last):
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip", line 8, in <module>
load_entry_point('pip==1.3.1', 'console_scripts', 'pip')()
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/__init__.py", line 149, in main
return command.main(args[1:], options)
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/basecommand.py", line 181, in main
logger.fatal('Storing complete log in %s' % log_fn)
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py", line 48, in fatal
self.log(self.FATAL, msg, *args, **kw)
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py", line 75, in log
backwardcompat.fwrite(consumer, rendered)
File "/home/wang/galaxy-dist/tool_deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/backwardcompat/__init__.py", line 88, in fwrite
f.write(s)
ValueError: I/O operation on closed file
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler ERROR 2014-12-17 14:38:54,807 Failed to do setup_virtualenv install, exit code='1'
I am working on SLES 11 SP3. Does anyone know how to fix this? On my OS X, there is no problem to install "join" into galaxy. Thanks,
Cheers,
Yu
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There is a Biostar site just for Galaxy. You'll probably have better luck posting this question there.
Thanks for pointing it out! I reposted it there.
OP posted question on the Galaxy Biostar after being made aware of it.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!